BMRB Entry 30694

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30694
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
The HADDOCK structure model of GDP KRas in complex with its allosteric inhibitor E22
Deposition date:
2019-12-04
Original release date:
2019-12-10
Authors:
Wang, X.; Gupta, A.; Prakash, P.; Putkey, J.; Gorfe, A.
Citation:

Citation: Gupta, A.; Wang, X.; Pagba, C.; Prakash, P.; Putkey, J.; Gorfe, A.. "Multi target ensemble based virtual screening yields novel allosteric KRAS inhibitors at high success rate"  Chem. Biol. Drug Des. 94, 1441-1456 (2019).
PubMed: 30903639

Assembly members:

Assembly members:
entity_1, polymer, 169 residues, 19271.760 Da.
entity_GDP, non-polymer, 443.201 Da.
entity_MG, non-polymer, 24.305 Da.
entity_QPD, non-polymer, 308.335 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MTEYKLVVVGAGGVGKSALT IQLIQNHFVDEYDPTIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHHYREQI KRVKDSEDVPMVLVGNKCDL PSRTVDTKQAQDLARSYGIP FIETSAKTRQGVDDAFYTLV REIRKHKEK

Data sets:
Data typeCount
15N chemical shifts160
1H chemical shifts160

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33
4entity_44

Entities:

Entity 1, entity_1 169 residues - 19271.760 Da.

1   METTHRGLUTYRLYSLEUVALVALVALGLY
2   ALAGLYGLYVALGLYLYSSERALALEUTHR
3   ILEGLNLEUILEGLNASNHISPHEVALASP
4   GLUTYRASPPROTHRILEGLUASPSERTYR
5   ARGLYSGLNVALVALILEASPGLYGLUTHR
6   CYSLEULEUASPILELEUASPTHRALAGLY
7   GLNGLUGLUTYRSERALAMETARGASPGLN
8   TYRMETARGTHRGLYGLUGLYPHELEUCYS
9   VALPHEALAILEASNASNTHRLYSSERPHE
10   GLUASPILEHISHISTYRARGGLUGLNILE
11   LYSARGVALLYSASPSERGLUASPVALPRO
12   METVALLEUVALGLYASNLYSCYSASPLEU
13   PROSERARGTHRVALASPTHRLYSGLNALA
14   GLNASPLEUALAARGSERTYRGLYILEPRO
15   PHEILEGLUTHRSERALALYSTHRARGGLN
16   GLYVALASPASPALAPHETYRTHRLEUVAL
17   ARGGLUILEARGLYSHISLYSGLULYS

Entity 2, entity_2 - C10 H15 N5 O11 P2 - 443.201 Da.

1   GDP

Entity 3, entity_3 - Mg - 24.305 Da.

1   MG

Entity 4, entity_4 - C17 H16 N4 O2 - 308.335 Da.

1   QPD

Samples:

sample_1: KRAS, [U-99% 13C; U-99% 15N], 0.8 mM; E22 1.0 mM; DTT, [U-99% 2H], 5 mM; DSS, [U-99% 2H], 10 uM; sodium phosphate, nature abundance, 25 mM; sodium chloride 50 mM; MAGNESIUM ION 5 mM

sample_2: E22 1.0 mM; DTT, [U-99% 2H], 5 mM; DSS, [U-99% 2H], 10 uM; sodium phosphate 25 mM; sodium chloride 50 mM; MAGNESIUM ION 5 mM; KRas, [U-99% 13C; U-99% 15N], 0.8 mM

sample_conditions_1: ionic strength: 115 mM; pH: 7.4; pressure: 1 Pa; temperature: 298 K

sample_conditions_2: ionic strength: 115 mM; pH: 7.4 pD; pressure: 1 Pa; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D NOESY 15N HSQCsample_1isotropicsample_conditions_1
2D 15N HSQCsample_1isotropicsample_conditions_1
2D 13C HSQCsample_2isotropicsample_conditions_2
3D CCH-TOCSYsample_2isotropicsample_conditions_2
3D NOESY 13C HSQCsample_2isotropicsample_conditions_2
F1 13C 15N filtered 3D NOESY 13C HSQCsample_2isotropicsample_conditions_2

Software:

TopSpin v2, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

HADDOCK, Bonvin - refinement, structure calculation

NMR spectrometers:

  • Bruker AVANCE 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks